Wrzodek, Clemens and Eichner, Johannes and Büchel, Finja and Zell, Andreas

InCroMAP: Integrated analysis of Cross-platform MicroArray and Pathway data.

Bioinformatics vol. 29 (2012), no. 4, pp. 506-508


Abstract

Microarrays are commonly used to detect changes in gene expression between different biological samples. For this purpose, many analysis tools have been developed that offer visualization, statistical analysis, and more sophisticated analysis methods. Most of these tools are designed specifically for messenger RNA microarrays. However today, more and more different microarray platforms are available. Changes in DNA methylation, microRNA expression or even protein phosphorylation states can be detected with specialized arrays. For these microarray technologies, the number of available tools is very small, compared to mRNA analysis tools. Especially, a joint analysis of different microarray platforms that have been employed on the same set of biological samples is hardly supported by most microarray analysis tools. We here present InCroMAP, a tool for the analysis and visualization of high-level microarray data from individual or multiple different platforms. Currently, InCroMAP supports mRNA, microRNA, DNA methylation and protein modification datasets. Several methods are offered that allow for an integrated analysis of data from those platforms. The available features of InCroMAP range from visualization of DNA methylation data over annotation of microRNA targets and integrated gene set enrichment analysis to a joint visualization of data from all platforms in the context of metabolic or signaling pathways. InCroMAP is freely available as Java application at http://www.cogsys.cs.uni-tuebingen.de/software/InCroMAP/, including a comprehensive user's guide and example files.


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BibTeX

@article{Wrzodek2012_3,
  author = {Wrzodek, Clemens and Eichner, Johannes and B\"uchel, Finja and Zell,
	Andreas},
  title = {{InCroMAP: Integrated analysis of Cross-platform MicroArray and Pathway
	data}.},
  journal = {Bioinformatics},
  year = {2012},
  volume = {29},
  pages = {506--508},
  number = {4},
  month = dec,
  abstract = {Microarrays are commonly used to detect changes in gene expression
	between different biological samples. For this purpose, many analysis
	tools have been developed that offer visualization, statistical analysis,
	and more sophisticated analysis methods. Most of these tools are
	designed specifically for messenger RNA microarrays. However today,
	more and more different microarray platforms are available. Changes
	in DNA methylation, microRNA expression or even protein phosphorylation
	states can be detected with specialized arrays. For these microarray
	technologies, the number of available tools is very small, compared
	to mRNA analysis tools. Especially, a joint analysis of different
	microarray platforms that have been employed on the same set of biological
	samples is hardly supported by most microarray analysis tools. We
	here present InCroMAP, a tool for the analysis and visualization
	of high-level microarray data from individual or multiple different
	platforms. Currently, InCroMAP supports mRNA, microRNA, DNA methylation
	and protein modification datasets. Several methods are offered that
	allow for an integrated analysis of data from those platforms. The
	available features of InCroMAP range from visualization of DNA methylation
	data over annotation of microRNA targets and integrated gene set
	enrichment analysis to a joint visualization of data from all platforms
	in the context of metabolic or signaling pathways. InCroMAP is freely
	available as Java application at \url{http://www.cogsys.cs.uni-tuebingen.de/software/InCroMAP/},
	including a comprehensive user's guide and example files.},
  doi = {10.1093/bioinformatics/bts709},
  eprint = {http://bioinformatics.oxfordjournals.org/content/29/4/506.full.pdf+html},
  keywords = {Integration of omics data, Integration, omics, data, Visualization,
	Microarray data, Pathway, Pathways, Data integration, Microarray
	data analysis, MicroRNA, InCroMAP, application, software},
  pdf = {http://bioinformatics.oxfordjournals.org/content/29/4/506.full.pdf},
  url = {http://bioinformatics.oxfordjournals.org/content/29/4/506}
}